Models AMBER

Fig. 1. The time evolution (top) and average cumulative difference (bottom) associated with the central dihedral angle of butane r (defined by the four carbon atoms), for trajectories differing initially in 10 , 10 , and 10 Angstoms of the Cartesian coordinates from a reference trajectory. The leap-frog/Verlet scheme at the timestep At = 1 fs is used in all cases, with an all-atom model comprised of bond-stretch, bond-angle, dihedral-angle, van der Waals, and electrostatic components, a.s specified by the AMBER force field within the INSIGHT/Discover program.

The AMBER (Assisted Model Building and Energy Refin emeni) is based on a force field developed for protein and nucleic acid computations by members of the Peter Kollman research group at the... 

Many of the torsional terms in the AMBER force field contain just one term from the cosine series expansion, but for some bonds it was found necessary to include more than one term. For example, to correctly model the tendency of O-C—C-O bonds to adopt a gauche conformation, a torsional potential with two terms was used for the O—C—C—O contribution ... 

Assisted model building with energy refinement (AMBER) is the name of both a force field and a molecular mechanics program. It was parameterized specifically for proteins and nucleic acids. AMBER uses only five bonding and nonbonding terms along with a sophisticated electrostatic treatment. No cross terms are included. Results are very good for proteins and nucleic acids, but can be somewhat erratic for other systems. 

YETI is a force held designed for the accurate representation of nonbonded interactions. It is most often used for modeling interactions between biomolecules and small substrate molecules. It is not designed for molecular geometry optimization so researchers often optimize the molecular geometry with some other force held, such as AMBER, then use YETI to model the docking process. Recent additions to YETI are support for metals and solvent effects. 

AMBER (assisted model building with energy refinement) a molecular mechanics force field... 

Another difference between the force fields is the calculation of electrostatic interactions. AMBER, BIO+, and OPLS use point charges to model electrostatic interactions. MM+ calculates electrostatic interactions using bond dipoles. The bond dipole method may not adequately simulate very polar or charged systems. 

P. A. KoUman and co-workers, AMBER Assisted Model Building and Energy Refinement, Urdversity of CaUforrda, San Erancisco, 1980—present ... 

AMBER (Assisted Model Building and Energy Refinement)... 

There is no well-defined way of calculating deprotonation energy with Amber. However, this does not matter as it totally cancels out in ONIOM by taking the difference between the real and model system. 

In the ONIOM(QM MM) scheme as described in Section 2.2, the protein is divided into two subsystems. The QM region (or model system ) contains the active-site selection and is treated by quantum mechanics (here most commonly the density functional B3LYP [31-34]). The MM region (referred to as the real system ) is treated with an empirical force field (here most commonly Amber 96 [35]). The real system contains the surrounding protein (or selected parts of it) and some solvent molecules. To analyze the effects of the protein on the catalytic reactions, we have in general compared the results from ONIOM QM MM models with active-site QM-only calculations. Such comparisons make it possible to isolate catalytic effects originating from e.g. the metal center itself from effects of the surrounding protein matrix. 

Figure 2-3. Protonated Schiff-base of retinal (PSBR) and computational models used in ONIOM QM QM calculations (left). Electrostatic effects of the surrounding protein on excitation energies in bacteriorhodopsin evaluated using TD-B3LYP Amber right). (Adapted from Vreven and Morokuma [37] (Copyright American Institute of Physics) and Vreven et al. [38], Reprinted with permission.)...

HF/STO-3G Amber - for R2met only). In all models the QM part consists of the two Fe centers and the first shell ligands of four formates, two imidazoles, and a few oxo, hydroxo, and/or aquo groups (see Figure 2-4). 

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